getBackgroundFrequencies: Get the four nucleotides background frequencies

Description Usage Arguments Author(s) Examples

View source: R/background.R

Description

Estimate the background frequencies of A,C,G,T on a set of promoters from an organism

Usage

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  getBackgroundFrequencies(organism = "dm3",
    pseudo.count = 1, quick = FALSE)

Arguments

organism

either a name of the organisms for which the background should be compiled (supported names are "dm3", "mm9" and "hg19"), a BSgenome object, DNAStringSet, or list of DNAString objects

pseudo.count

the number to which the frequencies sum up to, by default 1

quick

if to preform fitting on a reduced set of 100 promoters. This will not give as good results but is much quicker than fitting to all the promoters (~10k). Usage of this parameter is recommended only for testing and rough estimates.

Author(s)

Robert Stojnic, Diego Diez

Examples

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## Not run: 
  getBackgroundFrequencies("dm3")

## End(Not run)

PWMEnrich documentation built on May 2, 2018, 4:20 a.m.